BACKGROUND: Rats are an important experimental model for many human diseases. Many of these diseases have a genetic component. We are mapping the genomic locations of genes that regulate the development of experimental autoimmune arthritis and bone disorders in rats because it is highly likely that this information will facilitate the identification of similar genes or related biochemical pathways in humans, and may lead to novel therapies for various autoimmune and bone diseases. OBJECTIVES: This project has several components: 1) Development of dense genetic linkage, radiation hybrid, physical and transcription maps of the rat applicable to autoimmune disease-prone and disease-resistant inbred rat strains and to rat strains with and without bone disorders; 2) Development of comparative genomic maps among rats, mice and humans; 3) Generation and phenotypic characterization of experimental crosses of autoimmune disease-prone and disease-resistant inbred strains and of rat strains with and without bone defects; and 4) Linkage analysis to identify genomic regions containing disease regulatory genes. RESULTS: We have continued to work on the development of a dense genetic linkage map applicable to the rat strains in which we are interested (DA, LEW, BB (DR), F344, BN, ACI), concentrating on regions in which we identified disease regulatory genes. We previously reported the localization, by linkage techniques, of the rat osteopetrosis (op) mutation to the centromeric end of rat chromosome 10. We have continued our efforts to positionally clone the mutant op gene. Additional markers and additional intercross offspring with recombination events in the vicinity of the op gene were identified and the op gene is now mapped to a 0.5 cM interval. Development of a radiation hybrid map in this region has progressed. By homology with the human and mouse genomes, more than 40 mRNA transcripts have been identified in the region of the op gene, although with the most recent genetic map of its location, many of these genes are now likely outside the critical region. Several candidate genes in the op interval were evaluated by sequencing their coding regions, but mutations were not detected. We have also made substantial progress in mapping tl, a second, autosomal recessive, spontaneous mutation causing osteopetrosis in rats. Using 40 affected intercross offspring, we mapped the tl mutation to rat chromosome 2. Identification of the op and tl genes and characterization of their functional consequences are important because they appear to represent defects in osteoclast differentiation pathways that could suggest novel mechanisms to prevent bone destruction in inflammatory arthritis as well as to prevent bone density loss in post-menopausal women. Our second major focus has been to refine the locations of quantitative trait loci (QTLs) regulating phenotypes related to collagen-induced arthritis (CIA), adjuvant-induced arthritis (AIA) and other forms of experimental arthritis and related autoimmune diseases. For CIA, we have identified 20 QTLs (Cia1-20) that regulate disease severity. We have also identified 6 loci that regulate antibody titer (Ciaa1-6). For AIA, we have identified 6 QTLs (Aia1-6). Interestingly, QTLs on Chr4, Chr7, Chr10, Chr12 and Chr20 appear to be involved in the regulation of multiple experimental forms of autoimmune disease in rats, in addition to arthritis. The homologous locations in mice and humans also appear to contain regulatory genes for various forms of autoimmune diseases. During this past year we improved the radiation hybrid map of QTL regions on rat chromosomes 4 and 10. We also sequenced candidate genes from chromosomes 4 and 20 and identified polymorphisms among autoimmune disease prone and resistant rat strains. CONCLUSIONS: Current rat genetic resources are permitting both simple (osteopetrosis) and complex (experimental arthritis susceptibility) genetic traits to be successfully pursued in rat models. The genetic mapping data support our view that several QTLs harbor genes common to multiple autoimmune diseases. QTL-congenic rat strains are facilitating a much deeper analysis of the hypothesis that variant forms of several immunoregulatory genes play a role in multiple forms of autoimmune disease and may provide an explanation for "clustering" of distinct autoimmune diseases in families.